Hi Greg,
I want to use RDKit to quantify Shape Similarity between molecules and have
tried the following:
from rdkit.Chem import AllChem
mol1 = AllChem.MolFromSmiles("C(=O)(C(c1ccc(cc1)CC(C)C)C)NO")
AllChem.CanonicalizeMol(mol1)
AllChem.EmbedMolecule(mol1)
AllChem.UFFOptimizeMolecule(mol1)
AllChem.Kekulize(mol1)
mol2 = AllChem.MolFromSmiles("C(=O)(C(c1ccc(cc1)CC(C)C)C)NO")
AllChem.CanonicalizeMol(mol2)
AllChem.EmbedMolecule(mol2)
AllChem.UFFOptimizeMolecule(mol2)
AllChem.Kekulize(mol2)
print "Shape Tanimoto Distance: ", AllChem.ShapeTanimotoDist(mol1, mol2)
However, I have noticed that the similarity of a molecule to itself ranges
between 0.3 to 0.5 which doesn't seem OK. Is there something I am missing?
Also, can I get the tanimoto shape similarity between a molecule and a
pharmacophore?
Thanks
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